Package: nem

Version: 2.2.1

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check nem_2.2.1.tar.gz

RetCode: 0

Time: 124.2 seconds

Status: OK

CheckDir: nem.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/Users/biocbuild/bbs-2.1-bioc/meat/nem.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'nem/DESCRIPTION' ... OK
* this is package 'nem' version '2.2.1'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'nem' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
filterEGenes : clusterData: no visible global function definition for
  'silhouette'
nem: no visible global function definition for 'RelNet'
selectEGenes: no visible binding for global variable 'a'
selectEGenes: no visible binding for global variable 'b'
Found possibly global 'T' or 'F' in the following functions:
  bum.qalt qbum
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'moduleNetwork':
  print.ModuleNetwork

S3 methods shown with full name in documentation object 'pairwise.posterior':
  print.pairwise

S3 methods shown with full name in documentation object 'plot.effects':
  plot.effects

S3 methods shown with full name in documentation object 'plot.nem':
  plot.nem

S3 methods shown with full name in documentation object 'score':
  print.score

S3 methods shown with full name in documentation object 'triples.posterior':
  print.triples

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking data for non-ASCII characters ... OK
* creating nem-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating nem-manual.tex ... OK
* checking nem-manual.tex ... OK

* Installing *source* package 'nem' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: e1071
Loading required package: class
Loading required package: graph
Loading required package: Rgraphviz
Loading required package: RBGL

Attaching package: 'RBGL'


	The following object(s) are masked from package:e1071 :

	 extractPath 

Loading required package: time
** help
Note: unmatched right brace in 'nem.greedy' on or after line 41
 >>> Building/Updating help pages for package 'nem'
     Formats: text html latex example 
  BFSlevel                          text    html    latex   example
  BoutrosRNAi2002                   text    html    latex   example
  CONTmLL                           text    html    latex   example
  FULLmLL                           text    html    latex   example
  SCCgraph                          text    html    latex   example
  enumerate.models                  text    html    latex   example
  getDensityMatrix                  text    html    latex
  internal                          text    html    latex
  local.model.prior                 text    html    latex   example
  mLL                               text    html    latex   example
  moduleNetwork                     text    html    latex   example
  nem                               text    html    latex   example
  nem.cont.preprocess               text    html    latex   example
  nem.discretize                    text    html    latex   example
  nem.greedy                        text    html    latex   example
  nemModelSelection                 text    html    latex   example
  network.AIC                       text    html    latex   example
  pairwise.posterior                text    html    latex   example
  plot.effects                      text    html    latex   example
  plot.nem                          text    html    latex
  prune.graph                       text    html    latex   example
  score                             text    html    latex   example
  selectEGenes                      text    html    latex   example
  subsets                           text    html    latex   example
  transitive.closure                text    html    latex   example
  transitive.reduction              text    html    latex   example
  triples.posterior                 text    html    latex   example
** building package indices ...
* DONE (nem)